Job ID = 6366872 SRX = SRX245915 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:16 prefetch.2.10.7: 1) Downloading 'SRR765972'... 2020-06-15T23:09:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:59 prefetch.2.10.7: 1) 'SRR765972' was downloaded successfully Read 28225540 spots for SRR765972/SRR765972.sra Written 28225540 spots for SRR765972/SRR765972.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:37 28225540 reads; of these: 28225540 (100.00%) were unpaired; of these: 1616428 (5.73%) aligned 0 times 22167019 (78.54%) aligned exactly 1 time 4442093 (15.74%) aligned >1 times 94.27% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2684211 / 26609112 = 0.1009 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:23:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:34: 1000000 INFO @ Tue, 16 Jun 2020 08:23:39: 2000000 INFO @ Tue, 16 Jun 2020 08:23:44: 3000000 INFO @ Tue, 16 Jun 2020 08:23:49: 4000000 INFO @ Tue, 16 Jun 2020 08:23:54: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:23:59: 6000000 INFO @ Tue, 16 Jun 2020 08:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:23:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:04: 7000000 INFO @ Tue, 16 Jun 2020 08:24:05: 1000000 INFO @ Tue, 16 Jun 2020 08:24:09: 8000000 INFO @ Tue, 16 Jun 2020 08:24:11: 2000000 INFO @ Tue, 16 Jun 2020 08:24:15: 9000000 INFO @ Tue, 16 Jun 2020 08:24:17: 3000000 INFO @ Tue, 16 Jun 2020 08:24:20: 10000000 INFO @ Tue, 16 Jun 2020 08:24:23: 4000000 INFO @ Tue, 16 Jun 2020 08:24:26: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:24:29: 5000000 INFO @ Tue, 16 Jun 2020 08:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:24:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:31: 12000000 INFO @ Tue, 16 Jun 2020 08:24:35: 1000000 INFO @ Tue, 16 Jun 2020 08:24:35: 6000000 INFO @ Tue, 16 Jun 2020 08:24:36: 13000000 INFO @ Tue, 16 Jun 2020 08:24:40: 2000000 INFO @ Tue, 16 Jun 2020 08:24:41: 7000000 INFO @ Tue, 16 Jun 2020 08:24:42: 14000000 INFO @ Tue, 16 Jun 2020 08:24:45: 3000000 INFO @ Tue, 16 Jun 2020 08:24:47: 15000000 INFO @ Tue, 16 Jun 2020 08:24:47: 8000000 INFO @ Tue, 16 Jun 2020 08:24:51: 4000000 INFO @ Tue, 16 Jun 2020 08:24:52: 16000000 INFO @ Tue, 16 Jun 2020 08:24:53: 9000000 INFO @ Tue, 16 Jun 2020 08:24:56: 5000000 INFO @ Tue, 16 Jun 2020 08:24:57: 17000000 INFO @ Tue, 16 Jun 2020 08:24:58: 10000000 INFO @ Tue, 16 Jun 2020 08:25:01: 6000000 INFO @ Tue, 16 Jun 2020 08:25:03: 18000000 INFO @ Tue, 16 Jun 2020 08:25:04: 11000000 INFO @ Tue, 16 Jun 2020 08:25:07: 7000000 INFO @ Tue, 16 Jun 2020 08:25:08: 19000000 INFO @ Tue, 16 Jun 2020 08:25:10: 12000000 INFO @ Tue, 16 Jun 2020 08:25:12: 8000000 INFO @ Tue, 16 Jun 2020 08:25:13: 20000000 INFO @ Tue, 16 Jun 2020 08:25:16: 13000000 INFO @ Tue, 16 Jun 2020 08:25:18: 9000000 INFO @ Tue, 16 Jun 2020 08:25:19: 21000000 INFO @ Tue, 16 Jun 2020 08:25:22: 14000000 INFO @ Tue, 16 Jun 2020 08:25:23: 10000000 INFO @ Tue, 16 Jun 2020 08:25:24: 22000000 INFO @ Tue, 16 Jun 2020 08:25:28: 15000000 INFO @ Tue, 16 Jun 2020 08:25:29: 11000000 INFO @ Tue, 16 Jun 2020 08:25:30: 23000000 INFO @ Tue, 16 Jun 2020 08:25:34: 12000000 INFO @ Tue, 16 Jun 2020 08:25:34: 16000000 INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:25:35: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:25:35: #1 total tags in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:25:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:25:35: #1 tags after filtering in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:36: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 08:25:36: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2 alternative fragment length(s) may be 1,418,527,562 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05_model.r WARNING @ Tue, 16 Jun 2020 08:25:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:37: #2 You may need to consider one of the other alternative d(s): 1,418,527,562 WARNING @ Tue, 16 Jun 2020 08:25:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:25:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:39: 13000000 INFO @ Tue, 16 Jun 2020 08:25:40: 17000000 INFO @ Tue, 16 Jun 2020 08:25:45: 14000000 INFO @ Tue, 16 Jun 2020 08:25:46: 18000000 INFO @ Tue, 16 Jun 2020 08:25:50: 15000000 INFO @ Tue, 16 Jun 2020 08:25:52: 19000000 INFO @ Tue, 16 Jun 2020 08:25:56: 16000000 INFO @ Tue, 16 Jun 2020 08:25:58: 20000000 INFO @ Tue, 16 Jun 2020 08:26:01: 17000000 INFO @ Tue, 16 Jun 2020 08:26:04: 21000000 INFO @ Tue, 16 Jun 2020 08:26:07: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:10: 22000000 INFO @ Tue, 16 Jun 2020 08:26:12: 19000000 INFO @ Tue, 16 Jun 2020 08:26:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:16: 23000000 INFO @ Tue, 16 Jun 2020 08:26:18: 20000000 INFO @ Tue, 16 Jun 2020 08:26:22: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:26:22: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:26:22: #1 total tags in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:26:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:26:23: #1 tags after filtering in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:23: 21000000 INFO @ Tue, 16 Jun 2020 08:26:24: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 08:26:24: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:24: #2 alternative fragment length(s) may be 1,418,527,562 bps INFO @ Tue, 16 Jun 2020 08:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:24: #2 You may need to consider one of the other alternative d(s): 1,418,527,562 WARNING @ Tue, 16 Jun 2020 08:26:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:26:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:29: 22000000 INFO @ Tue, 16 Jun 2020 08:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:34: 23000000 INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:26:39: #1 total tags in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:26:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:26:39: #1 tags after filtering in treatment: 23924901 INFO @ Tue, 16 Jun 2020 08:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:41: #2 number of paired peaks: 166 WARNING @ Tue, 16 Jun 2020 08:26:41: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:41: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:41: #2 alternative fragment length(s) may be 1,418,527,562 bps INFO @ Tue, 16 Jun 2020 08:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20_model.r WARNING @ Tue, 16 Jun 2020 08:26:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:41: #2 You may need to consider one of the other alternative d(s): 1,418,527,562 WARNING @ Tue, 16 Jun 2020 08:26:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:26:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX245915/SRX245915.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling